Tag Archives: mitochondrial dna

This story starts in Italy and will then take us to the Tarim Basin in Northwestern China. It features a well-known mummy (Oetzi) and one of the best preserved mummies in the world (The Beauty of Xiaohe). It contains data from in-depth DNA analysis performed on one mummy and holds the promise of similar date generated in the near future on another set of mummies. Fasten your seatbelts, here we go.

During the month of August 2010, several stories hit the wire that the DNA of Oetzi, the famous Iceman mummy had been sequenced. The Iceman was discovered emerging from a glacier on the border between Austria and Italy. His mitochondrial DNA is now the oldest complete H. sapiens mtDNA genome generated to date.

This is where we segue to the Tarim Basin mummies, discovered thousands of miles away from the Alps. As it turns out, Oetzi’s find spot was very close to Alpine pastures where Dr. Victor Mair’s family once took their animals to graze, and that brings us to the Tarim Basin Mummies, a long term focus of Dr. Mair’s research.

A gratuitous link between these two areas, you say? Not necessarily, if one considers what has just been announced in Italy and the potential of what could happen with the mummies in China. Moreover, one of the reasons Dr. Mair got to be so interested in ancient human remains was the discovery of Oetzi in 1991. This occurred a few years after he had seen the Tarim Basin mummies on display in a museum in Urumqi.

The Beauty of Xiaohe. Courtesy of the Xinjiang Uyghur Autonomous Region Museum in Urumqi.

Oetzi lived about 5000 years ago; while the Beauty of Xiaohe lived about 1,000 years later, around 2000 BC. In both cases, DNA research has been carried out on these early human remains. It seems that the Beauty of Xiaohe and her kinfolk had very close links with areas to the west of the Pamir Mountains. (In a previous blog, the Pamirs are mentioned as part of the geography of the Xinjiang Uyghur Autonomous Region). Specifically, “Mitochondrial DNA analysis showed that the Xiaohe people carried both the East Eurasian haplogroup (C) and the West Eurasian haplogroups (H and K), whereas chromosomal DNA analysis revealed only the West Eurasian haplogroup R1a1a in the male individuals.”

Oetzi is of European origin; the Tarim Basin Mummies are often referred to as Eurasian, and Caucasian, without much further information about where they may have originated from, other than “west of the Pamir mountains.” This is where the reference made above, to the potential of future research comes in. The techniques exist to investigate the Tarim Basin mummies in much greater detail. The research has not happened yet.

In addition, there are ways to establish where individuals were born and raised, one of the most famous examples being the remains of an archer found close to Stonehenge. Tests showed that he originated in the Alps, probably Switzerland, Austria or Germany. He somehow made his way into what is now the United Kingdom, where he was buried. A similar scientific approach could be applied to the Xiaohe remains. I am sure that one day this will happen.

Don’t miss Secrets of the Silk Road, open now at HMNS. See strikingly well-preserved mummies, tall in stature and fair in complexion, that have lain in the parched Tarim Basin of western China for 3,800 years along with 150 objects drawn from the Xinjiang Uygur Autonomous Region Museum and the Xinjiang Institute of Archaeology in Urumqi.

In the summer of 2008, a multi-national team of Russian, European and American researchers found a small bone at a remote cave site in Siberia. At the time of discovery researchers had been working at the Denisova cave, located in the Altai Mountains in southern Siberia for several years already. Moreover, the cave was open to visitors as early as 2000, when it was listed on the program of The Second International Conference on Bioinformatics of Genome Regulation and Structure, held in Novosibirsk.

Initially, the discovery of a bone did not raise eyebrows, as the presence of Neanderthal people in the area between 48,000 and 30,000 years ago was a well-established fact. Interesting thus far, but nothing out of the ordinary.

As it turns out the small bone, identified as one of the bones in one’s pinky, held some surprises. Scientists at the Max Planck Institute in Leipzig extracted DNA – specifically mitochondrial DNA — and concluded that this type of DNA represented “a hitherto unknown type of hominin mtDNA that shares a common ancestor with anatomically modern human and Neanderthal mtDNAs about 1.0 million years ago.” [For those scratching their head over the term “hominin,” this refers to extinct members of the human lineage.] So we are looking at one bone of a previously unknown hominin? Possibly. Or maybe not.

The notion that we had several hominins living side by side, modern humans, Neanderthalers, and possibly this third species, should not come as a surprise. This happened quite frequently in our past; our existence today as the sole representatives of the human lineage is seen as an exception rather than the rule. What would be remarkable is that we have evidence of a human ancestor or close relative whom we did not know existed.

The latter realization has created a lot of buzz among those interested in human evolution. As is always the case with this type of endeavor, we need to be cautious and outline what we know, what the limits of our understanding are and where we shift from scientifically supportable reconstructions to pure speculation. A number of topics need further clarification here.

First, where does the owner of the bone fit in on the family tree, especially compared to us and to Neanderthals?

Location of Denisova Cave and presumed place
on the family tree of the Denisova Cave specimen.

Researchers compared the Denisova mitochondrial DNA to complete mitochondrial sequences from 54 modern humans as well as a human who lived in Siberia about 30,000 years ago, six Neanderthals from more than 40,000 years ago, a modern pygmy chimpanzee and a modern common chimp. The results indicated that there are about 400 differences between us and the DNA in the pinky. This is twice as many differences as exist between modern human and Neanderthal DNA. This has led researchers to suggest that our last common ancestor lived about 1 million years ago, about twice as long ago as the common ancestor to us and Neanderthalers.

A second question that begs an answer is: “what creature does this DNA belong to?” Various scenarios have been suggested here. It is possible, that we are dealing with a new species, neither modern human nor Neanderthal. Secondly, it could be a Neanderthal child, resulting from a union between a Neanderthal and an unknown species. Lastly it could be a Neanderthal individual, carrying variations in genetic make up thus far not identified in predominantly European samples.

The possibility that we are dealing with a completely new species is the most exciting. It is also one that most people caution us against. “Too soon,” “not enough material,” are some of the more common reactions. Others disagree and support the notion that this is a different species. This argument between those who see few species in the archaeological record (“lumpers”) and those who prefer a larger number of species (“splitters”) is one that has been described in a previous blog.

The scenario raising the possibility of an interspecies affair (between Neanderthal and another species) is favored by some, who see parallels with an alleged Neanderthal – modern human hybrid child found in Portugal. In this case, however, we would be looking at a child of a Neanderthal and a yet unknown species. This still implies that we had an unknown creature wandering the Siberian wilds, one whose genetics were inherited by a mixed offspring. In other words, this scenario still requires acceptance of the existence of an unknown species.

Finally it is conceivable that the breath of Neanderthal genetic variation is such that we have not mapped all of it. Given that most research on Neanderthals has concentrated on European materials, rather than Siberian, perhaps these Eastern Neanderthals carried in them a number of genetic variations that hark back to the original population in Africa. This would support the third option, one which identifies this pinky bone as belonging to a Neanderthal individual, albeit it with genetic markers not encountered in European samples. If identified as such, then this bone would reinforce the notion that Neanderthals occupied a much larger territory than originally assumed.

This discovery is meaningful in several ways. It illustrates that science marches on, providing answers to questions and, in the process, raises additional questions. It also shows how meticulous one has to work as an archaeologist or paleoanthropologist. One small pinky bone has provided us with a “what-in-the-world-is-this?” moment. The decision to perform a DNA test warns us not to be complacent. Up until recently, the party line about who was around some 40,000 years ago would have been answered with Homo sapiens or Neanderthalers, and nobody else. We are now forced to entertain the possibility of a hitherto unknown species living side by side with the other two. That is the promise this one tiny pinky bone holds.

A few final comments and thoughts.

What most articles I have read do not elaborate on is the fact that research is now happening in Siberia. This is a huge territory, difficult to access for all kinds of reasons. When discoveries like these are made, we should not be surprised that they generate questions we cannot answer yet, as researchers are accessing a territory close to the size of the US (a fact appreciated more than a century ago). I hope this discovery will result in greater support for research in the region. One day I am sure we will have a much clearer picture of what it is we are dealing with here.

Recently I came across several examples of how genetic information has greatly helped us understand the past. Quite often this data is gathered in the most unexpected places. Consider these examples.

In an article published in December 2009, an international group of scientists addresses the issue of the extinction of North American megafauna traditionally dated some 11,000 years ago. A skeleton of a woolly mammoth on display in a museum never fails to impress us. At the same time, most of us would agree that it is a good thing we don’t have to worry any more about these lumbering giants messing up our evening commute. However, what most of us stop worrying about is when these animals became extinct and why. Most of us, that is, but not all of us. This is where the story of ancient DNA retrieved from perennially frozen soil comes in.

A traditional approach to estimate when and where a species became extinct has been to map and date the last known survivors. The thinking was that knowing when and where the last specimens lived would automatically clue us in as to why they died out. Is this true, however? Do these last known survivors really represent that last ones left standing? Or did we miss them and make wrong assumptions?

The party line about woolly mammoths was that they survived on remote islands in the far northern regions of Alaska and Siberia, a region referred to as Beringia. That is now old hat. New genetic data tells us a different story. Mammoths may have survived much longer than originally thought in the Alaskan interior. Scratch 13,000 years ago. Now it looks like woolly mammoths may have survived for an additional 2,600 to 3,700 years in parts of Alaska. Mitochondrial DNA was retrieved from perennially frozen soil near Stevens Village in the Yukon Flat. What we have here then is a suggestion that we can establish the presence of certain animals in a region at a certain time in the past. No bones needed. Just animal DNA left behind in the soil and preserved because of the permanent frozen condition of the dirt.

While the researchers were careful to address any shortcomings of their approach (contamination of the soil, migration of more ancient DNA from lower-lying areas to more recent layers closer to the surface), there will be reactions from other members in the scientific community. This may be frustrating to those among us who like to see “the final answer” to questions like these, this dialogue is part of what science is all about. We will have to see if these new results will stand up to the criticism that will come.

As megafauna slowly disappeared from the North American landscape, human settlers were making their presence felt. I have written about the questions of where these earlier migrants into the Americas may have come from. There is very good evidence that the Paleoindians migrated from parts of Asia.

It turns out that we all have a copy of this virus residing within us. It is harmless to most of us, unless your immune system is compromised. Geneticists studying this virus found that it was remarkably stable and very rarely mutated into a new variety. Moreover, the strain of the JC virus carried by the Navajo today is nearly identical to that carried by the modern inhabitants of Tokyo. The JC virus bolsters an Asian origin theory for the First Americans.

Beringia – Image courtesy of NASA.

As to how Paleoindians arrived into the Americas, genetics can help us focus that picture as well. If one accepts that the Bering Strait was an ancient migration route – and most people have no problem accepting this – then the issue is: exactly what route did they follow? A coastal route and an interior, overland route, often suggested by archaeologists, now both seem to have been used.

North American mitochondrial DNA, collected from contemporary populations, points to two migration routes. In a paper published Jan. 19, 2009, scientists studied various mitochondrial DNA haplogroups, zooming in on two rare groups. One of these (known as D4h3) is found only along the Pacific coast and is mostly in South America, while the second group (X2a) is restricted to northern North America.

The presence of X2a in North America east of the Rocky Mountains may support the idea of an ice-free corridor between two ice sheets covering Canada and parts of the US. Some of the earliest migrants may have followed that route which would have taken them into the Great Plains, where the glacial corridor would have ended. The presence of D4h3 along the Pacific may represent a coastal migration route.

Woolly mammoths leaving their DNA in the soil, viruses carried by all of us and DNA shared through the mother’s family line all help us refine and refute some of the ideas on how the first immigrants arrived in the Americas. I am sure genetics will continue to add to our understanding of this momentous period in human history. Stay tuned.